People seem to over-estimate Good Boo and Innocent Boo due to their feats against Pure Boo and Goku SSj3. However, there is much more going on then meets the eye.
I went over Goku's fight with Innocent Boo before, and for the first issue, it was more-or-less just Goku buying some time and not really taking the fight seriously at all. Innocent Boo only managed to land a single punch on him because Goku was thinking about how Majin Boo can learn any move rather quickly.
This one-sided fight continues on to the opening of the following issue, where Goku opens with a cross to his face, and Innocent Boo returns with one of his. But the artwork still shows that Goku is completely non-chalant. Goku did perform a Kamehameha wave, but as we see during his fight with Pure Boo, Goku requires at least 1 full minute to gather his Ki in order to unleash a fully powered Kamehameha wave; the one he performed against Innocent Boo likely had the amount of effort that he was putting into the fight, none at all.
So the fight continues and Goku is still learning about Majin Boo's weird anatomy and how quickly he can learn new attacks. Which surprises him when Boo performs a Kamehameha wave. Goku knocks it back and Majin Boo decides to knock it in the direction opposite to Goku, giving him no time to stop it. Babadi was always standing behind Boo and the artwork shows that this is what happened. Think of it as the time when Nappa was about to murder Gohan and Krillen and a more powerful Goku was unable to close the distance between himself and Nappa.
The evidence is here:
Pay attention to where Babadi is in comparison to Majin Boo before and after the explosion.
Finally, Goku ends the fight because he no longer has to buy any time and compliments Boo about his ability to instantly learn anybodies fighting techniques.
As a final wrap-up, I didn't see any evidence to support the claim that these two were actually close in power at that time. If there was, well... I didn't see it.
There is nothing wrong with Goku being 2.5x stronger than Innocent Boo at all, and Innocent Boo simultaneously being 2.5x stronger than Teen Gohan. This would actually make much more sense considering how Vegeta was able to at least resist Majin Boo to some degree. I seriously believe that Majin Boo's energy radar is completely accurate, why else would Toriyama place it there?
@Kaboom
1) There's talk at one or two points about Boo being awoken and released early, which wouldn't be possible if the energy being gathered was required to wake him at all, right?
2) Building on that, Kaioshin warns that if that happens, Boo would still be able to kill them all and destroy Earth even if he doesn't have all the energy he needs.
3) When the energy meter is suddenly full, Bobbidi actually yells, "Boo is at full power!" At least he does in Viz's translation, but that's such a simple expression I doubt they'd screw it up...
4) Finally, SS2 Gohan's power being "almost half" of Fat Boo's actually lines up really darn well with how Boo and the Super Saiyan 2s seemed to compare in combat.
In regards to Good Boo vs Pure Boo, Pure Boo was able to effortlessly tool Good Boo durnig their entire bout'. The gap between both of these Boo's is so tremendous that it's reflective of the gap between Freeza vs Base Goku and Vegetto vs Boohan. Other-wise, Good Boo wouldn't be tooled the way he was. He only managed to land a head-butt and an additional punch. This is essentially reflective of what Vegeta was capable of, he landed two attacks but nothing more. Good Boo's infinite stamina and regeneration allow him to take more a pummelling. So him being greater then Vegeta SSj2 in terms of battle power isn't entirely justified by what was depicted within Good Boo's fight against Pure Boo.
@Kaboom
Good Boo really didn't do any better against Pure Boo than Vegeta combat-wise. He just lasted longer because he can regenerate.
That's what gives any form of Majin Boo an advantage over other people to begin with. He's rubbery and resilient, and it's hard to damage him permanently because he can instantly and repeatedly just regrow himself. Vegeta only went down more quickly because he can't do those things. He can't "bounce back" the way Mister Boo could.
Let me put it this way... If Boo were stronger than Vegeta, but COULDN'T regenerate... could he have survived this?